Hi Anthony, There are no known problems with the gene/codon BED tool, but if you have an example of a problem, I will take a look. Some items to double check first: 1 - Input is a BED 12 file 2 - Keep in mind that coordinates are "0-based, half-open start, fully closed end" and always reported with respect to the forward strand. Notation for bases 1-100 of a sequence would be written as: [0,100) More details are at: http://wiki.g2.bx.psu.edu/Learn/Datatypes#Bed 3 - This can make the math a bit tricky for transcripts aligning to the negative strand. This wiki by Angie at UCSC is definitely the best at explaining how to manipulate this type of data: http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms If you still think there is an issue, create a simple test of just a single or few transcripts with the problems in a dataset, run the tool, then tell me what you think is exactly wrong. Share the history using "Options" (gear icon) -> Share or publish -> generate a share link, copy, and send that back along with your comments to to my email address directly (only). Simple is best, so that we can narrow down the exact issue. For the aaChanges, this tool will work with most native Galaxy reference genomes (the tool group name is confusing, sorry!). Just set the build to be the same for all inputs. Stick with full builds (not variants - e.g. use mm9, not mm9female). If you get an error about a missing build, write back and I can let you know if the build is native or not, or possibly even add it to the index if it was previously excluded for some reason that no longer applies. Custom reference genomes are not available for this tool, so if it does turn out that the public Galaxy instance cannot make your particular build available, a local install would be the alternative: http://getgalaxy.org If you work out the gene/codon BED coordinates based on the additional info, please reply to the list to let us know. If not, I'll just watch for your shared link, Best, Jen Galaxy team On 7/11/12 2:07 PM, Antony Jose wrote:

Hi, When using the gene BED to codon BED tool, I noticed that it is not accurately reporting the codons that make up a gene. For example, some of the codon are missing (particularly ones that span exon-exon junctions. Also, when changing reading frame from one exon to the next, the codons are not read appropriately and the reading frame appears to be decided arbitrarily. Is this a serious known flaw with the tool or am I missing something? Also, is there a version of aaChanges tool that can be used with any genome (not just human genome?). Thank you. Antony

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